Sandbox1257

'''This sandbox is in use until June 1, 2009 for UMass Chemistry 490a. Others please do not edit this page. Thanks!'''

DNA:RNA interactions
The shown representation is a DNA:RAN hybrid duplex. This is the DNA in orange and this is the RNA in green. Notice that all hydrogen bonds between the bases are linear. We can choose to see the base pairs, which show very neatly. First, the G-C pairs: dG-C are in blue and dC-G are in yellow. Similarly, we can see the dA-U in red and the dT-A in purple (note that the RNA has U nucleotides instead of T). Furthermore, we can also see the purine and pyrimidine bonding with each other (never with themselves) for a more general view of the bases. In this generic RNA:DNA hybrid all hydrogen bonds between the bases are through the Watson Crick faces, as shown for the dG-C pair. If we choose to see the ions in the hybrid, as we'd expect, the whole complex shines: the backbone and the nucleotides are negatively charged.

Reference
http://www.rcsb.org/pdb/explore.do?structureId=124d